5mkq - Revision history

OCA at 18:48, 1 November 2023

OCA — Wed, 01 Nov 2023 18:48:22 GMT

←Older revision		Revision as of 18:48, 1 November 2023
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	<StructureSection load='5mkq' size='340' side='right'caption='[[5mkq]], [[Resolution\|resolution]] 2.79Å' scene=''>		<StructureSection load='5mkq' size='340' side='right'caption='[[5mkq]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mkq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.79Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mkq OCA], [~~http~~://pdbe.org/5mkq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mkq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mkq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mkq ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mkq OCA], [https://pdbe.org/5mkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mkq RCSB], [https://www.ebi.ac.uk/pdbsum/5mkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mkq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TTUA_PYRHO TTUA_PYRHO] Catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T) (PubMed:28655838). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (By similarity). Can use free sulfide as sulfur source in vitro, which may be also the sulfur source in vivo (PubMed:28655838).[UniProtKB:Q72LF3]<ref>PMID:28655838</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arragain, S]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: Bimai, O]]	+	[[Category: Arragain S]]
-	[[Category: Golinelli-Pimpaneau, B]]	+	[[Category: Bimai O]]
-	[[Category: Legrand, P]]	+	[[Category: Golinelli-Pimpaneau B]]
-	~~[[Category: 4fe-4]]~~	+	[[Category: Legrand P]]
-	~~[[Category: Anomal]]~~	+
-	~~[[Category: Apo]]~~	+
-	~~[[Category: Fe-edge]]~~	+
-	~~[[Category: Iron-sulfur cluster]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ph0300]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Trna modification]]~~	+
-	~~[[Category: Trna thiolation]]~~	+
-	~~[[Category: Ttua~~]]	+

OCA at 07:21, 19 August 2020

OCA — Wed, 19 Aug 2020 07:21:58 GMT

←Older revision		Revision as of 07:21, 19 August 2020
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	==TtuA enzyme containing a [4Fe-4S]==		==TtuA enzyme containing a [4Fe-4S]==
-	<StructureSection load='5mkq' size='340' side='right' caption='[[5mkq]], [[Resolution\|resolution]] 2.79Å' scene=''>	+	<StructureSection load='5mkq' size='340' side='right'caption='[[5mkq]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mkq OCA], [http://pdbe.org/5mkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mkq RCSB], [http://www.ebi.ac.uk/pdbsum/5mkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mkq ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mkq OCA], [http://pdbe.org/5mkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mkq RCSB], [http://www.ebi.ac.uk/pdbsum/5mkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mkq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arragain, S]]		[[Category: Arragain, S]]
	[[Category: Bimai, O]]		[[Category: Bimai, O]]

OCA at 09:01, 3 August 2017

OCA — Thu, 03 Aug 2017 09:01:28 GMT

←Older revision		Revision as of 09:01, 3 August 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5mkq is ~~ON HOLD~~	+	==TtuA enzyme containing a [4Fe-4S]==
		+	<StructureSection load='5mkq' size='340' side='right' caption='[[5mkq]], [[Resolution\|resolution]] 2.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MKQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mkq OCA], [http://pdbe.org/5mkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mkq RCSB], [http://www.ebi.ac.uk/pdbsum/5mkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mkq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Sulfur is present in several nucleosides within tRNAs. In particular, thiolation of the universally conserved methyl-uridine at position 54 stabilizes tRNAs from thermophilic bacteria and hyperthermophilic archaea and is required for growth at high temperature. The simple nonredox substitution of the C2-uridine carbonyl oxygen by sulfur is catalyzed by tRNA thiouridine synthetases called TtuA. Spectroscopic, enzymatic, and structural studies indicate that TtuA carries a catalytically essential [4Fe-4S] cluster and requires ATP for activity. A series of crystal structures shows that (i) the cluster is ligated by only three cysteines that are fully conserved, allowing the fourth unique iron to bind a small ligand, such as exogenous sulfide, and (ii) the ATP binding site, localized thanks to a protein-bound AMP molecule, a reaction product, is adjacent to the cluster. A mechanism for tRNA sulfuration is suggested, in which the unique iron of the catalytic cluster serves to bind exogenous sulfide, thus acting as a sulfur carrier.

-	~~Authors: Arragain~~, S., Bimai, O., Legrand, P., Golinelli-Pimpaneau, B.	+	Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.,Arragain S, Bimai O, Legrand P, Caillat S, Ravanat JL, Touati N, Binet L, Atta M, Fontecave M, Golinelli-Pimpaneau B Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7355-7360. doi:, 10.1073/pnas.1700902114. Epub 2017 Jun 27. PMID:28655838<ref>PMID:28655838</ref>

-	~~Description: TtuA enzyme containing~~ a ~~[4Fe-4S]~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Golinelli-Pimpaneau, B]]~~	+	<div class="pdbe-citations 5mkq" style="background-color:#fffaf0;"></div>
-	~~[[Category: Legrand, P]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Arragain, S]]		[[Category: Arragain, S]]
	[[Category: Bimai, O]]		[[Category: Bimai, O]]
		+	[[Category: Golinelli-Pimpaneau, B]]
		+	[[Category: Legrand, P]]
		+	[[Category: 4fe-4]]
		+	[[Category: Anomal]]
		+	[[Category: Apo]]
		+	[[Category: Fe-edge]]
		+	[[Category: Iron-sulfur cluster]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Ph0300]]
		+	[[Category: Rna]]
		+	[[Category: Trna modification]]
		+	[[Category: Trna thiolation]]
		+	[[Category: Ttua]]

OCA at 11:24, 9 March 2017

OCA — Thu, 09 Mar 2017 11:24:12 GMT

←Older revision		Revision as of 11:24, 9 March 2017
Line 7:		Line 7:
	Description: TtuA enzyme containing a [4Fe-4S]		Description: TtuA enzyme containing a [4Fe-4S]
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Golinelli-Pimpaneau, B]]
	[[Category: Legrand, P]]		[[Category: Legrand, P]]
	[[Category: Arragain, S]]		[[Category: Arragain, S]]
	[[Category: Bimai, O]]		[[Category: Bimai, O]]
-	[[Category: Golinelli-Pimpaneau, B]]

OCA: Protected "5mkq" [edit=sysop:move=sysop]

OCA — Thu, 15 Dec 2016 16:25:20 GMT

Protected "5mkq" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:25, 15 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mkq is ON HOLD Authors: Arragain, S., Bimai, O., Legrand, P., Golinelli-Pimpaneau, B. Description: TtuA enzyme containing a [4Fe-4S] [[Category: U...

OCA — Thu, 15 Dec 2016 16:25:18 GMT

New page: '''Unreleased structure''' The entry 5mkq is ON HOLD Authors: Arragain, S., Bimai, O., Legrand, P., Golinelli-Pimpaneau, B. Description: TtuA enzyme containing a [4Fe-4S] [[Category: U...

New page

'''Unreleased structure'''

The entry 5mkq is ON HOLD

Authors: Arragain, S., Bimai, O., Legrand, P., Golinelli-Pimpaneau, B.

Description: TtuA enzyme containing a [4Fe-4S]
[[Category: Unreleased Structures]]
[[Category: Legrand, P]]
[[Category: Arragain, S]]
[[Category: Bimai, O]]
[[Category: Golinelli-Pimpaneau, B]]